The complete mitochondrial genome of Ophiocordyceps gracilis and its comparison with related species

Abuduaini, Aifeire; Wang, Yuanbing; Zhou, Huiying; Kang, Ruiping; Ding, Mei; Yu, Jing; Suo, Feiya; Huang, Luodong

doi:10.1186/s43008-021-00081-z

Cited by 8 publications

(6 citation statements)

References 65 publications

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“…The cox 1 gene showed the largest variation among all PCGs because of abundant introns. The presence/absence of introns indicated that introns were related to the evolutionary dynamics of mitotic introns [ 6 ]. Subsequently, the duplication of the tRNAs of the C .…”

Section: Discussionmentioning

confidence: 99%

“…The fungal mitogenome contains 14 protein-coding genes (PCGs) ( nad 1-6, nad 4L, cob , cox 1-3, atp 6, atp 8 and atp 9) that are related to electron transport and oxidative phosphorylation in the inner membrane of mitochondria. It also includes the mitochondrial 16S ribosomal small subunit RNA gene ( rrns ), the mitochondrial 23S ribosomal large subunit RNA gene ( rrnl ) and a variety of tRNA genes necessary for translation [ 6 ].…”

Section: Introductionmentioning

confidence: 99%

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De novo mitochondrial genome sequencing of Cladonia subulata and phylogenetic analysis with other dissimilar species

Fang,

Mamut,

Wang

et al. 2023

PLoS ONE

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In this study, the complete mitochondrial genome of Cladonia subulata (L.) FH Wigg was sequenced and assembled and then compared with those of other Cladonia species. The mitogenome of Cladonia subulata, the type species of Cladonia, consisted of a circular DNA molecule of 58,895 bp 44 genes (15 protein-coding genes, 2 rRNA genes, and 27 tRNA genes). The base composition had shown an obvious AT preference, and all 27 tRNA genes formed a typical clover structure. Comparison with other 7 Cladonia species indicated that the duplication/loss of tRNAs had occurred during evolution, and introns appeared to explain the variation in cox1 genes in Cladonia, the mitochondrial genome tends to be generally conservative and local dynamic changes. Repeat sequences were mainly located in gene intervals, which were mainly distributed among intergenic spacers and may cause rearrangement of the mitogenome. The phylogenetic results showed that Cladonia subulata and C. polycarpoides were assigned to the Cladonia Subclade. The results add to the available mitochondrial genome sequence information of Cladonia subulata, provide basic data for the systematic development, resource protection, and genetic diversity research in Cladonia subulata, and also provide theoretical support for further genomic research of lichens.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

De novo mitochondrial genome sequencing of Cladonia subulata and phylogenetic analysis with other dissimilar species

Fang,

Mamut,

Wang

et al. 2023

PLoS ONE

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“…Due to its high copy number and rapidly conserved inherited genetic functions, as well as its fast evolution, mitochondrial DNA (mt-DNA) has been extensively acknowledged as a molecular marker present in the evolutionary trees of a large number of fungi and mushrooms [ 3 ]. Through the study of ascomycetes, researchers have discovered that mt-DNAs are usually circular and significantly encoded by the same DNA strand [ 4 ].…”

Section: Introductionmentioning

confidence: 99%

Mitogenomic and Phylogenetic Analysis of the Entomopathogenic Fungus Ophiocordyceps lanpingensis and Comparative Analysis with Other Ophiocordyceps Species

Bibi

Wang

et al. 2023

Genes

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Ophiocordyceps lanpingensis (O. lanpingensis) belongs to the genus Ophiocordyceps, which is often found in Yunnan Province, China. This species is pharmacologically important for the treatment of renal disorders induced by oxidative stress and an inadequate immune response. In the present study, the mitogenome of O. lanpingensis was determined to be a circular molecule 117,560 bp in length, and to have 31% G + C content and 69% A + T content. This mitogenome comprised 82% of the whole genome that codes for significant genes. The protein-coding regions of the O. lanpingensis mitogenome, containing 24 protein-coding genes, were associated with respiratory chain complexes, such as 3 ATP-synthase complex F0 subunits (atp6, atp8, and atp9), 2 complex IV subunits/cytochrome c oxidases (cox2 and cox3), 1 complex III subunit (cob), 4 electron transport complex I subunits/NADH dehydrogenase complex subunits (nad1, nad4, nad5, and nad6), 2 ribosomal RNAs (rns, rnl), and 11 hypothetical/predicted proteins, i.e., orf609, orf495, orf815, orf47, orf150, orf147, orf292, orf127, orf349, orf452, and orf100. It was noted that all genes were positioned on the same strand. Further, 13 mitochondrial genes with respiratory chain complexes, which presented maximum similarity with other fungal species of Ophiocordyceps, were investigated. O. lanpingensis was compared with previously sequenced species within Ophiocordycepitaceae. Comparative analysis indicated that O. lanpingensis was more closely related to O. sinensis, which is one of the most remarkable and expensive herbs due to its limited availability and the fact that it is difficult to culture. Therefore, O. lanpingensis is an important medicinal resource that can be effectively used for medicinal purposes. More extensive metabolomics research is recommended for O. lanpingensis.

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“…Mitochondrial genome is called the ‘second genome’ of eukaryotes, which is considered to be obtained from bacteria through endosymbiosis (Gray et al 2001 ). Independent origin, single parent inheritance and several available molecular markers make the mitogenome an effective tool to infer the phylogenetic relationship of species (Abuduaini et al 2021 ; Basse 2010 ). In addition, mitochondrial gene arrangement, variation of conserved genes, dynamic changes of introns, structural variation of tRNA, codon usage and so on also provide rich genetic information for the analysis of species variation and evolution (Fonseca et al 2021 ; Ren et al 2021 ; Wu et al 2021a ; Zhang et al 2021a ).…”

Section: Introductionmentioning

confidence: 99%

The first two mitochondrial genomes for the genus Ramaria reveal mitochondrial genome evolution of Ramaria and phylogeny of Basidiomycota

Zhang

et al. 2022

IMA Fungus

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In the present study, we assembled and analyzed the mitogenomes of two Ramaria species. The assembled mitogenomes of Ramaria cfr. rubripermanens and R. rubella were circularized, with sizes of 126,497 bp and 143,271 bp, respectively. Comparative mitogenome analysis showed that intron region contributed the most (contribution rate, 43.74%) to the size variations of Ramaria mitogenomes. The genetic contents, gene length, tRNAs, and codon usages of the two Ramaria mitogenomes varied greatly. In addition, the evolutionary rates of different core protein coding genes (PCGs) in Phallomycetidae mitogenomes varied. We detected large-scale gene rearrangements between Phallomycetidae mitogenomes, including gene displacement and tRNA doubling. A total of 4499 bp and 7746 bp aligned fragments were detected between the mitochondrial and nuclear genomes of R. cfr. rubripermanens and R. rubella, respectively, indicating possible gene transferring events. We further found frequent intron loss/gain and potential intron transfer events in Phallomycetidae mitogenomes during the evolution, and the mitogenomes of R. rubella contained a novel intron P44. Phylogenetic analyses using both Bayesian inference (BI) and Maximum Likelihood (ML) methods based on a combined mitochondrial gene dataset obtained an identical and well-supported phylogenetic tree for Basidiomycota, wherein R. cfr. rubripermanens and Turbinellus floccosus are sister species. This study served as the first report on mitogenomes from the genus Ramaria, which provides a basis for understanding the evolution, genetics, and taxonomy of this important fungal group.

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The complete mitochondrial genome of Ophiocordyceps gracilis and its comparison with related species

Cited by 8 publications

References 65 publications

De novo mitochondrial genome sequencing of Cladonia subulata and phylogenetic analysis with other dissimilar species

De novo mitochondrial genome sequencing of Cladonia subulata and phylogenetic analysis with other dissimilar species

Mitogenomic and Phylogenetic Analysis of the Entomopathogenic Fungus Ophiocordyceps lanpingensis and Comparative Analysis with Other Ophiocordyceps Species

The first two mitochondrial genomes for the genus Ramaria reveal mitochondrial genome evolution of Ramaria and phylogeny of Basidiomycota

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